Identifying microorganisms which fill a niche similar to that of the pathogen: a new investigative approach for discovering biological control organisms

Understanding the mechanisms of suppressive soils should lead to the development of new strategies to manage pests and diseases. For suppressive soils that have a biological nature, one of the first steps in understanding them is to identify the organisms contributing to this phenomenon. Here we present a new approach for identifying microorganisms involved in soil suppressiveness. This strategy identifies microorganisms that fill a niche similar to that of the pathogen by utilizing substrate utilization assays in soil. To demonstrate this approach, we examined an avocado grove where a Phytophthora cinnamomi epidemic created soils in which the pathogen could not be detected with baiting techniques, a characteristic common to many soils with suppressiveness against P. cinnamomi. Substrate utilization assays were used to identify rRNA genes (rDNA) from bacteria that rapidly grew in response to amino acids known to attract P. cinnamomi zoospores. Six bacterial rDNA intergenic sequences were prevalent in the epidemic soils but uncommon in the non-epidemic soils. These sequences belonged to bacteria related to Bacillus mycoides, Renibacterium salmoninarum, and Streptococcus pneumoniae. We hypothesize that bacteria such as these, which respond to the same environmental cues that trigger root infection by the pathogen, will occupy a niche similar to that of the pathogen and contribute to suppressiveness through mechanisms such as nutrient competition and antibiosis.